Programs

These are the programs that need to be installed and included locally.

library(gridExtra)
library(knitr)
library(ggplot2)
#install.packages("fastqcr")
library(fastqcr)
fastqc_install()

Only Modify This Chunk

This is the only chunk that needs modification when reusing this script with different datasets. The later chunks produce outputs based on the directory locations listed here.

## assign directory locations

# the full path to the .fast.gz files for each sample:
fq.dir<-"/storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/lil_samples"

# the full path for outputs
qc.dir<-"/storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control"

Run fastqc

Only run this code once when first working on the files. The outputs are a html and a zip file for each sample. When these are produced, you don’t need to produce them again if you rerun the code further down. This is why this chunk is temporarily commented out.

#fastqc(fq.dir = fq.dir, # FASTQ files directory
#       qc.dir = qc.dir, # Results directory
#       threads = 4      # Number of threads
#       )
# list the files in the output directory to ensure success (if you want)
#list.files(qc.dir)
# a better way to check success is to compare the number of files
# first list the number of samples files
length(list.files(fq.dir, pattern = "*.fastq.gz"))
## [1] 109
# and see if it matches the number of output zip files
length(list.files(qc.dir, pattern = "*.zip"))
## [1] 109

Quality Plots for Each Sample

# create a vector with the samples names, taken from the output files
samps<-list.files(qc.dir, full.names = T, pattern = "*.zip")

#plot qc test results for each sample
for (i in samps){
  #read info for given sample from the .zip file generated in the previous step
  samp.info <- qc_read(i)
  #open blank list to hold qc visualizations for the given sample
  plot<-list()
  #do qc for the given sample
  plot[[1]]<-qc_plot(samp.info, "Basic statistics")
  plot[[2]]<-qc_plot(samp.info, "Per sequence quality scores")
  plot[[3]]<-qc_plot(samp.info, "Sequence duplication levels")
  #visualize tables
  print(paste0("QC results for sample ", gsub(".*/", "", i)))

  cat('\n')

  print(kable(plot[[1]]))

  cat('\n')

  #visualize plots
  grid.arrange(plot[[2]],plot[[3]],
               ncol=2)
  
  #clear plot to hold info for next sample
  rm(plot)
}
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_127_fastqc.zip
## [1] "QC results for sample Hlil_127_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_127.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |71024                   |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |54                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_130_fastqc.zip

## [1] "QC results for sample Hlil_130_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_130.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2003627                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |54                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_132_fastqc.zip

## [1] "QC results for sample Hlil_132_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_132.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2236334                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |54                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_135_fastqc.zip

## [1] "QC results for sample Hlil_135_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_135.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |545242                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |56                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_137_fastqc.zip

## [1] "QC results for sample Hlil_137_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_137.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1572141                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_143_fastqc.zip

## [1] "QC results for sample Hlil_143_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_143.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1490633                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_145_fastqc.zip

## [1] "QC results for sample Hlil_145_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_145.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1446751                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_146_fastqc.zip

## [1] "QC results for sample Hlil_146_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_146.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |816769                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |57                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_147_fastqc.zip

## [1] "QC results for sample Hlil_147_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_147.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |4651854                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |54                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_148_fastqc.zip

## [1] "QC results for sample Hlil_148_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_148.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1888604                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |55                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_150_fastqc.zip

## [1] "QC results for sample Hlil_150_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_150.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |3066462                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |55                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_152_fastqc.zip

## [1] "QC results for sample Hlil_152_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_152.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2712705                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_153_fastqc.zip

## [1] "QC results for sample Hlil_153_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_153.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2591356                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_154_fastqc.zip

## [1] "QC results for sample Hlil_154_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_154.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1674461                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_155_fastqc.zip

## [1] "QC results for sample Hlil_155_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_155.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |914366                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |54                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_156_fastqc.zip

## [1] "QC results for sample Hlil_156_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_156.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1307126                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |58                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_157_fastqc.zip

## [1] "QC results for sample Hlil_157_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_157.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1089297                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_158_fastqc.zip

## [1] "QC results for sample Hlil_158_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_158.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1541016                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |56                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_159_fastqc.zip

## [1] "QC results for sample Hlil_159_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_159.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1734326                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |56                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_160_fastqc.zip

## [1] "QC results for sample Hlil_160_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_160.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1083021                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |55                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_161_fastqc.zip

## [1] "QC results for sample Hlil_161_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_161.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1866482                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_162_fastqc.zip

## [1] "QC results for sample Hlil_162_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_162.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1654937                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_163_fastqc.zip

## [1] "QC results for sample Hlil_163_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_163.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2633376                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |54                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_164_fastqc.zip

## [1] "QC results for sample Hlil_164_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_164.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2837977                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_165_fastqc.zip

## [1] "QC results for sample Hlil_165_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_165.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |4609865                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_166_fastqc.zip

## [1] "QC results for sample Hlil_166_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_166.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2830748                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_168_fastqc.zip

## [1] "QC results for sample Hlil_168_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_168.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1307980                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_169_fastqc.zip

## [1] "QC results for sample Hlil_169_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_169.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |4133873                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_173_fastqc.zip

## [1] "QC results for sample Hlil_173_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_173.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2630072                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_174_fastqc.zip

## [1] "QC results for sample Hlil_174_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_174.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |3683216                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_175_fastqc.zip

## [1] "QC results for sample Hlil_175_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_175.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1946397                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_176_fastqc.zip

## [1] "QC results for sample Hlil_176_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_176.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2606430                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_177_fastqc.zip

## [1] "QC results for sample Hlil_177_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_177.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2108701                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_178_fastqc.zip

## [1] "QC results for sample Hlil_178_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_178.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2648953                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_179_fastqc.zip

## [1] "QC results for sample Hlil_179_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_179.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2642622                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_180_fastqc.zip

## [1] "QC results for sample Hlil_180_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_180.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |3374155                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_181_fastqc.zip

## [1] "QC results for sample Hlil_181_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_181.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |421595                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_182_fastqc.zip

## [1] "QC results for sample Hlil_182_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_182.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2317930                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_183_fastqc.zip

## [1] "QC results for sample Hlil_183_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_183.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |802234                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_184_fastqc.zip

## [1] "QC results for sample Hlil_184_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_184.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |650295                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |55                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_185_fastqc.zip

## [1] "QC results for sample Hlil_185_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_185.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1025935                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_186_fastqc.zip

## [1] "QC results for sample Hlil_186_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_186.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |551799                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_188_fastqc.zip

## [1] "QC results for sample Hlil_188_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_188.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1198003                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_189_fastqc.zip

## [1] "QC results for sample Hlil_189_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_189.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |415025                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_190_fastqc.zip

## [1] "QC results for sample Hlil_190_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_190.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1063764                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_191_fastqc.zip

## [1] "QC results for sample Hlil_191_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_191.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1174120                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_192_fastqc.zip

## [1] "QC results for sample Hlil_192_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_192.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |111094                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_193_fastqc.zip

## [1] "QC results for sample Hlil_193_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_193.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1665511                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_195_fastqc.zip

## [1] "QC results for sample Hlil_195_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_195.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |217625                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_196_fastqc.zip

## [1] "QC results for sample Hlil_196_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_196.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2097876                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_197_fastqc.zip

## [1] "QC results for sample Hlil_197_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_197.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1205600                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_198_fastqc.zip

## [1] "QC results for sample Hlil_198_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_198.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |970559                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_199_fastqc.zip

## [1] "QC results for sample Hlil_199_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_199.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1034547                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_200_fastqc.zip

## [1] "QC results for sample Hlil_200_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_200.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1010091                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_201_fastqc.zip

## [1] "QC results for sample Hlil_201_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_201.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |627998                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_202_fastqc.zip

## [1] "QC results for sample Hlil_202_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_202.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1274612                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_203_fastqc.zip

## [1] "QC results for sample Hlil_203_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_203.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1391584                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_204_fastqc.zip

## [1] "QC results for sample Hlil_204_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_204.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |741691                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_205_fastqc.zip

## [1] "QC results for sample Hlil_205_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_205.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1569870                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_206_fastqc.zip

## [1] "QC results for sample Hlil_206_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_206.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |298080                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |57                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_207_fastqc.zip

## [1] "QC results for sample Hlil_207_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_207.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2746727                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_208_fastqc.zip

## [1] "QC results for sample Hlil_208_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_208.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |219015                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_209_fastqc.zip

## [1] "QC results for sample Hlil_209_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_209.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1626053                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_210_fastqc.zip

## [1] "QC results for sample Hlil_210_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_210.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1609485                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_211_fastqc.zip

## [1] "QC results for sample Hlil_211_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_211.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1175159                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_212_fastqc.zip

## [1] "QC results for sample Hlil_212_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_212.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |259017                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_213_fastqc.zip

## [1] "QC results for sample Hlil_213_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_213.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1411565                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_214_fastqc.zip

## [1] "QC results for sample Hlil_214_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_214.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2057978                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_215_fastqc.zip

## [1] "QC results for sample Hlil_215_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_215.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |738322                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_216_fastqc.zip

## [1] "QC results for sample Hlil_216_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_216.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |958785                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_217_fastqc.zip

## [1] "QC results for sample Hlil_217_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_217.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |307499                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_218_fastqc.zip

## [1] "QC results for sample Hlil_218_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_218.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |617199                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_219_fastqc.zip

## [1] "QC results for sample Hlil_219_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_219.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2358499                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_220_fastqc.zip

## [1] "QC results for sample Hlil_220_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_220.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |939542                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_221_fastqc.zip

## [1] "QC results for sample Hlil_221_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_221.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |448543                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_224_fastqc.zip

## [1] "QC results for sample Hlil_224_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_224.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1325242                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_225_fastqc.zip

## [1] "QC results for sample Hlil_225_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_225.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |481073                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_226_fastqc.zip

## [1] "QC results for sample Hlil_226_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_226.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1145517                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_227_fastqc.zip

## [1] "QC results for sample Hlil_227_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_227.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |236877                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_228_fastqc.zip

## [1] "QC results for sample Hlil_228_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_228.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |595712                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_229_fastqc.zip

## [1] "QC results for sample Hlil_229_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_229.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |676317                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_230_fastqc.zip

## [1] "QC results for sample Hlil_230_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_230.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |129535                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |54                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_231_fastqc.zip

## [1] "QC results for sample Hlil_231_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_231.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1238697                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_232_fastqc.zip

## [1] "QC results for sample Hlil_232_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_232.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |743479                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_233_fastqc.zip

## [1] "QC results for sample Hlil_233_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_233.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1065394                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_234_fastqc.zip

## [1] "QC results for sample Hlil_234_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_234.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |114929                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_235_fastqc.zip

## [1] "QC results for sample Hlil_235_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_235.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1700592                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_236_fastqc.zip

## [1] "QC results for sample Hlil_236_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_236.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |347630                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_237_fastqc.zip

## [1] "QC results for sample Hlil_237_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_237.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |209300                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_238_fastqc.zip

## [1] "QC results for sample Hlil_238_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_238.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |488277                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_239_fastqc.zip

## [1] "QC results for sample Hlil_239_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_239.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |333793                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_240_fastqc.zip

## [1] "QC results for sample Hlil_240_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_240.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |655178                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_241_fastqc.zip

## [1] "QC results for sample Hlil_241_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_241.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |674262                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_242_fastqc.zip

## [1] "QC results for sample Hlil_242_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_242.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |820807                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_243_fastqc.zip

## [1] "QC results for sample Hlil_243_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_243.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |2356281                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_244_fastqc.zip

## [1] "QC results for sample Hlil_244_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_244.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1045211                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_245_fastqc.zip

## [1] "QC results for sample Hlil_245_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_245.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |622481                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_246_fastqc.zip

## [1] "QC results for sample Hlil_246_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_246.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1180373                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_247_fastqc.zip

## [1] "QC results for sample Hlil_247_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_247.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1142556                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_248_fastqc.zip

## [1] "QC results for sample Hlil_248_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_248.fastq.gz       |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1005973                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |57                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NBG_351_fastqc.zip

## [1] "QC results for sample Hlil_NBG_351_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_NBG_351.fastq.gz   |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1644600                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NC_167_fastqc.zip

## [1] "QC results for sample Hlil_NC_167_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_NC_167.fastq.gz    |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |3093287                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NC_170_fastqc.zip

## [1] "QC results for sample Hlil_NC_170_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_NC_170.fastq.gz    |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1123578                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NC_171_fastqc.zip

## [1] "QC results for sample Hlil_NC_171_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_NC_171.fastq.gz    |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |5068513                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NC_172_fastqc.zip

## [1] "QC results for sample Hlil_NC_172_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_NC_172.fastq.gz    |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |3926228                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |51                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_NTBG_260_fastqc.zip

## [1] "QC results for sample Hlil_NTBG_260_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_NTBG_260.fastq.gz  |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |1749198                 |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |52                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_W_222_fastqc.zip

## [1] "QC results for sample Hlil_W_222_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_W_222.fastq.gz     |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |753330                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_W_223_fastqc.zip

## [1] "QC results for sample Hlil_W_223_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_W_223.fastq.gz     |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |716338                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |53                      |
## Reading: /storage1/fs1/christine.e.edwards/Active/mashburn/Hibiscus/1_Hlil/stacks/quality_control/Hlil_WBG_226_fastqc.zip

## [1] "QC results for sample Hlil_WBG_226_fastqc.zip"
## 
## 
## 
## |Measure                           |Value                   |
## |:---------------------------------|:-----------------------|
## |Filename                          |Hlil_WBG_226.fastq.gz   |
## |File type                         |Conventional base calls |
## |Encoding                          |Sanger / Illumina 1.9   |
## |Total Sequences                   |324748                  |
## |Sequences flagged as poor quality |0                       |
## |Sequence length                   |36                      |
## |%GC                               |54                      |

Aggregate Report

This is an aggregate report; it produces a table with some summary stats for each sample.

#aggregate the reports by pointing this function to the folder holding the output files
qc <- qc_aggregate(qc.dir, progressbar = F)
## Warning: `select_()` is deprecated as of dplyr 0.7.0.
## Please use `select()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
#stats per sample
knitr::kable(qc_stats(qc))
sample pct.dup pct.gc tot.seq seq.length
Hlil_127 66.94 54 71024 36
Hlil_130 94.07 54 2003627 36
Hlil_132 94.73 54 2236334 36
Hlil_135 84.20 56 545242 36
Hlil_137 94.61 53 1572141 36
Hlil_143 93.86 53 1490633 36
Hlil_145 90.38 53 1446751 36
Hlil_146 85.70 57 816769 36
Hlil_147 95.88 54 4651854 36
Hlil_148 89.46 55 1888604 36
Hlil_150 92.17 55 3066462 36
Hlil_152 94.50 52 2712705 36
Hlil_153 94.25 52 2591356 36
Hlil_154 91.75 52 1674461 36
Hlil_155 90.62 54 914366 36
Hlil_156 84.17 58 1307126 36
Hlil_157 88.71 52 1089297 36
Hlil_158 90.83 56 1541016 36
Hlil_159 92.05 56 1734326 36
Hlil_160 87.28 55 1083021 36
Hlil_161 92.48 52 1866482 36
Hlil_162 92.66 53 1654937 36
Hlil_163 94.44 54 2633376 36
Hlil_164 95.02 53 2837977 36
Hlil_165 97.28 51 4609865 36
Hlil_166 95.77 52 2830748 36
Hlil_168 94.10 53 1307980 36
Hlil_169 96.47 53 4133873 36
Hlil_173 95.10 53 2630072 36
Hlil_174 96.51 52 3683216 36
Hlil_175 95.80 53 1946397 36
Hlil_176 96.59 52 2606430 36
Hlil_177 94.48 52 2108701 36
Hlil_178 94.89 53 2648953 36
Hlil_179 95.44 52 2642622 36
Hlil_180 96.92 51 3374155 36
Hlil_181 87.72 52 421595 36
Hlil_182 93.99 52 2317930 36
Hlil_183 91.57 52 802234 36
Hlil_184 83.34 55 650295 36
Hlil_185 90.23 53 1025935 36
Hlil_186 89.42 53 551799 36
Hlil_188 89.68 53 1198003 36
Hlil_189 87.94 53 415025 36
Hlil_190 91.35 52 1063764 36
Hlil_191 91.45 52 1174120 36
Hlil_192 73.92 53 111094 36
Hlil_193 92.23 52 1665511 36
Hlil_195 83.38 53 217625 36
Hlil_196 93.92 51 2097876 36
Hlil_197 91.69 51 1205600 36
Hlil_198 92.49 52 970559 36
Hlil_199 91.70 51 1034547 36
Hlil_200 91.14 51 1010091 36
Hlil_201 90.01 53 627998 36
Hlil_202 91.74 51 1274612 36
Hlil_203 92.50 51 1391584 36
Hlil_204 88.54 52 741691 36
Hlil_205 91.95 51 1569870 36
Hlil_206 77.65 57 298080 36
Hlil_207 94.83 52 2746727 36
Hlil_208 79.84 53 219015 36
Hlil_209 92.25 53 1626053 36
Hlil_210 91.61 52 1609485 36
Hlil_211 91.48 51 1175159 36
Hlil_212 82.83 53 259017 36
Hlil_213 91.52 51 1411565 36
Hlil_214 93.27 51 2057978 36
Hlil_215 90.79 52 738322 36
Hlil_216 90.78 52 958785 36
Hlil_217 85.51 53 307499 36
Hlil_218 91.41 52 617199 36
Hlil_219 94.19 51 2358499 36
Hlil_220 89.66 53 939542 36
Hlil_221 90.25 51 448543 36
Hlil_224 92.59 51 1325242 36
Hlil_225 89.79 53 481073 36
Hlil_226 91.55 52 1145517 36
Hlil_227 85.54 52 236877 36
Hlil_228 89.69 52 595712 36
Hlil_229 91.30 51 676317 36
Hlil_230 81.05 54 129535 36
Hlil_231 93.36 51 1238697 36
Hlil_232 92.02 52 743479 36
Hlil_233 92.54 51 1065394 36
Hlil_234 79.91 52 114929 36
Hlil_235 92.99 51 1700592 36
Hlil_236 88.37 52 347630 36
Hlil_237 84.20 52 209300 36
Hlil_238 90.44 52 488277 36
Hlil_239 88.90 53 333793 36
Hlil_240 87.67 52 655178 36
Hlil_241 91.34 51 674262 36
Hlil_242 91.77 53 820807 36
Hlil_243 93.98 52 2356281 36
Hlil_244 90.42 52 1045211 36
Hlil_245 89.22 52 622481 36
Hlil_246 91.51 52 1180373 36
Hlil_247 90.83 52 1142556 36
Hlil_248 83.95 57 1005973 36
Hlil_NBG_351 94.01 51 1644600 36
Hlil_NC_167 95.93 53 3093287 36
Hlil_NC_170 93.56 53 1123578 36
Hlil_NC_171 97.12 53 5068513 36
Hlil_NC_172 97.00 51 3926228 36
Hlil_NTBG_260 94.34 52 1749198 36
Hlil_W_222 90.11 53 753330 36
Hlil_W_223 90.70 53 716338 36
Hlil_WBG_226 79.69 54 324748 36

Summary Figures for All Samples

In the following figures: - the solid red line = median sample value - the dashed red line = 10% of median value

#save stats info as an object
stats.info<-qc_stats(qc)
#make tot.seq numeric
stats.info$tot.seq<-as.numeric(stats.info$tot.seq)

#make histogram of number of sequence reads for each sample
ggplot(stats.info, aes(x=tot.seq))+
              geom_histogram(color="black", fill="white", bins=20)+
              geom_vline(aes(xintercept=median(tot.seq)), color = "red")+
              geom_vline(aes(xintercept=median(tot.seq)*.1), color = "red", lty=14)+
              theme_classic()+
              xlab("Number of sequencing reads")

#solid red line = median sample value
#dashed red line = 10% of median sample value
ggplot(stats.info, aes(x=tot.seq))+
              geom_histogram(color="black", fill="white", bins=200)+
              geom_vline(aes(xintercept=median(tot.seq)), color = "red")+
              geom_vline(aes(xintercept=median(tot.seq)*.1), color = "red", lty=14)+
              theme_classic()+
              xlab("Number of sequencing reads")

Samples to Drop

The samples to drop are selected as having less than 10% of the median reads.

#show me the samples that have less than 10% of the number of reads as the median sample from this experiment (these should be dropped immediately)
print(paste("Median sample contains", median(stats.info$tot.seq), "reads. The following samples contain less than", median(stats.info$tot.seq)*.1, "reads (10% of the median), and should likely be dropped"))
## [1] "Median sample contains 1175159 reads. The following samples contain less than 117515.9 reads (10% of the median), and should likely be dropped"
knitr::kable(stats.info[stats.info$tot.seq < median(stats.info$tot.seq)*.1,])
sample pct.dup pct.gc tot.seq seq.length
Hlil_127 66.94 54 71024 36
Hlil_192 73.92 53 111094 36
Hlil_234 79.91 52 114929 36